Research

1Body Atlas: New query terms available.

Curious about gene expression patterns in a particular tissue or cell line? Now you can search Body Atlas with tissue and cell line queries to find tissue and cell line- related gene expression and mutational information.

Try a query for a tissue term to find overall gene expression levels in the tissue or find genes specifically enriched in the queried tissue. Or, try a query with a cell line to find overall gene expression and cell-line specific amplifications, deletions and mutations.

2 My data: Studies and projects in a single location.

The new "My Data" tab merges "My Studies" and "My Projects" so you can access both studies and projects from a single location. All data previously imported or saved in studies or projects are now accessible through "My Data". Just click on the tabs within "My Data" to switch between viewing your studies or projects. Studies can still be filtered by organisms, data types, keywords and more.

3 Query API: New APIs for atlases, genetic markers and biogroups

Six new commands are available in the Query API.

• bodyatlas: Returns a list of tissues, cell types, stem cells and cell lines ranked by relevance for the queried gene, biogroup, or bioset.
• diseaseatlas: Returns a list of diseases, traits, conditions, and surrogate endpoints associated with a gene, SNP or biogroup.
• knockdownatlas: Finds genes whose perturbation affects your query term.
• pharmacoatlas: Finds compounds and treatments significantly correlated to a gene or biogroup.
• geneticmarkers: Returns a ranked list of genes significantly correlated to a phenotype, tissue, or compound.
• biogroups: Returns biogroups for which a queried phenotype, tissue, or compound is highly enriched.

(The Query API is available to NextBio Enterprise users.)

4 NextBio Research: More data, more answers.

We're proud to announce major changes to NextBio Basic and Professional.

• Update of the user interface to the "Vertical Apps" redesign (made available to NextBio Enterprise users in January 2011).
• Access to over 2,000 additional studies from new data types, including GWAS, CNVs, mutation data, epigenetics, and more.
• Use of Genome Browser and Meta-Analysis apps, previously available only to Enterprise users.
• NextBio Basic is now called NextBio Public.

NextBio Public is free to users from academic, government, and non-profit research institutions. Visit our Product Comparison page to learn more about our products and why you should upgrade to NextBio Professional.

Why did we redesign our interface? Learn more:

• Data-driven capabilities

4 NextBio Research: More data, more answers.

Data-driven capabilities.

Our data-driven features and functions are now accessible as apps from the top of every page, making it easier for you to explore correlations derived from public genomic data.

How does this help you? NextBio's expert curation and data analysis let you access in an instant what would take a team of bioinformaticians and scientists months-or years-to build from scratch. We precompute data correlations across thousands of curated, publicly available genomic studies, allowing you to find answers to your biological questions from meta-analyses performed on actual experimental datasets. You can also securely import private experimental data, and use NextBio to expand your understanding of biological mechanisms of interest.

Learn more:

• Apps = answers

4 NextBio Research: More data, more answers.

Apps = answers.

Each NextBio app answers a specific biological question about your query term. For example, to answer the question "Which diseases are correlated with the gene POU5F2?" query Disease Atlas.

Just type "POU5F2" in the query field at the top of any page, then click the Disease Atlas icon above it. You'll receive a list of experimental datasets in which POU5F2 is mutated, differentially expressed, or otherwise significant. Your list will be categorized by disease according to NextBio's disease ontology.

Learn more:

• Ease of navigation

4 NextBio Research: More data, more answers.

Ease of navigation.

Want to ask many biological questions about a single query term? You can now switch views just by clicking an app's icon. (No need to go back to the original results page.) But if you want to ask the same question about many different biological terms, just enter a new query term. You'll query the current app and receive new results in the same layout.

5 NextBio Research: Explore the apps.

QuickView

Not sure where to begin? Get a comprehensive overview of everything NextBio can tell you about your query term or imported dataset.

• QuickView
• Curated Studies
• Body Atlas
• Disease Atlas
• Pharmaco Atlas
• Knockdown Atlas
• Genetic Markers
• Biogroups
• Genome Browser
• Literature
• Clinical Trials

5 NextBio Research: Explore the apps.

Curated Studies

Access our continuously growing library of curated public genomic data. Query this app to see how your query term or imported dataset correlate with thousands of curated public studies.

• QuickView
• Curated Studies
• Body Atlas
• Disease Atlas
• Pharmaco Atlas
• Knockdown Atlas
• Genetic Markers
• Biogroups
• Genome Browser
• Literature
• Clinical Trials

5 NextBio Research: Explore the apps.

Body Atlas

Compare gene expression levels across hundreds of human and mouse tissues, cell types, cell lines, and stem cells.

• QuickView
• Curated Studies
• Body Atlas
• Disease Atlas
• Pharmaco Atlas
• Knockdown Atlas
• Genetic Markers
• Biogroups
• Genome Browser
• Literature
• Clinical Trials

5 NextBio Research: Explore the apps.

Disease Atlas

Find diseases that are significantly correlated to a gene or imported dataset.

• QuickView
• Curated Studies
• Body Atlas
• Disease Atlas
• Pharmaco Atlas
• Knockdown Atlas
• Genetic Markers
• Biogroups
• Genome Browser
• Literature
• Clinical Trials

5NextBio Research: Explore the apps.

Pharmaco Atlas

Discover drugs and compounds whose genetic signature includes a particular gene or is enriched in an imported dataset.

• QuickView
• Curated Studies
• Body Atlas
• Disease Atlas
• Pharmaco Atlas
• Knockdown Atlas
• Genetic Markers
• Biogroups
• Genome Browser
• Literature
• Clinical Trials

5 NextBio Research: Explore the apps.

Knockdown Atlas

Perform knockdown, knockout, or overexpression experiments in reverse: See which genetic perturbations affect a gene or imported dataset, and how.

• QuickView
• Curated Studies
• Body Atlas
• Disease Atlas
• Pharmaco Atlas
• Knockdown Atlas
• Genetic Markers
• Biogroups
• Genome Browser
• Literature
• Clinical Trials

5 NextBio Research: Explore the apps.

Genetic Markers

Discover genes & SNPs found to be significant across multiple studies of a disease, compound, or tissue.

• QuickView
• Curated Studies
• Body Atlas
• Disease Atlas
• Pharmaco Atlas
• Knockdown Atlas
• Genetic Markers
• Biogroups
• Genome Browser
• Literature
• Clinical Trials

5 NextBio Research: Explore the apps.

Biogroups

Find pathways, molecular functions, protein families, and biological processes that involve a gene or are enriched in an imported dataset.

• QuickView
• Curated Studies
• Body Atlas
• Disease Atlas
• Pharmaco Atlas
• Knockdown Atlas
• Genetic Markers
• Biogroups
• Genome Browser
• Literature
• Clinical Trials

5 NextBio Research: Explore the apps.

Genome Browser

Build a visual map of how experimental results line up with genomic elements, CNVs, SNPs, miRNA targets, and more.

• QuickView
• Curated Studies
• Body Atlas
• Disease Atlas
• Pharmaco Atlas
• Knockdown Atlas
• Genetic Markers
• Biogroups
• Genome Browser
• Literature
• Clinical Trials

5 NextBio Research: Explore the apps.

Literature

Do a classic PubMed literature search, or search hundreds of biology- and health-related news sources.

• QuickView
• Curated Studies
• Body Atlas
• Disease Atlas
• Pharmaco Atlas
• Knockdown Atlas
• Genetic Markers
• Biogroups
• Genome Browser
• Literature
• Clinical Trials

5 NextBio Research: Explore the apps.

Clinical Trials

Find clinical trials that interest you (including actively recruiting studies).

• QuickView
• Curated Studies
• Body Atlas
• Disease Atlas
• Pharmaco Atlas
• Knockdown Atlas
• Genetic Markers
• Biogroups
• Genome Browser
• Literature
• Clinical Trials